2 years, Engineer-level bioinformatics fixed-term contract, Starting Autum 2026
Supervision Anne-Violette Lavoir – ISA Institut Sophia Agrobiotech – Equipe MIB, Centre INRAE-PACA, Sophia Antipolis & Nicolas Francillonne URGI INRAE Versailles
Localisation: ISA Institut Sophia Agrobiotech, Sophia Antipolis
CONTEXT – As part of the European project ECOGREATION and the French project METASERV, the partners proposed to inventory the digital tools used in relation to service plants (databases, decision support systems, predictive models, etc.) and to develop a tool, as comprehensive as possible, to help identify and establish a service plant within a given agroecosystem. The ecosystem service initially targeted is pest regulation (biocontrol plants), particularly through the promotion of their natural enemies within the system1.
To identify candidate plant species with the potential to promote the establishment and persistence of natural enemies of crop pests in greenhouse agroecosystems, the ISA partner has developed a dedicated database that compiles numerous examples of service plants used for pest regulation through the enhancement of natural enemy communities: The Biocontrol Plant Database2 of INRAE (BP-DB, https://isaceaweb.sophia.inra.fr/bp_dss_dev/). The tool helps to generate a preliminary list of service plants that have already demonstrated their effectiveness in pest suppression by supporting the abundance, diversity, or activity of natural enemies within the cropping system. Yet, the tool is not efficient enough.
OBJECTIVE –
1. The database will be reviewed and refined by identifying potential improvements through comparison with existing tools and ongoing projects. Furthermore, the recruited engineer will update the database through the incorporation of recently published data and findings from the scientific literature.
2. The recruited enginer will also test a digital tool based on AI technology, originally designed to identify molecules from metabolomic data in the literature (METABIOMICS, developed by the team led by LF Nothias, Institut 3IA, UniCA, Tysinger et al. 2023). It will be trained on the scientific literature on PdS with the aim of extracting data demonstrating the ability of PdS to regulate pest populations selected in the project or, conversely, data invalidating the functionality of PdS (identified disservices). The AI outputs will be compared with the BP-DB analysis carried out in the previous sub-task, in order to see to what extent these two approaches are functional and/or complement each other.
3. Finally, the last objective will be to identify the multifunctional aspects of the selected plant species. For this purpose, selection criteria (ecosystem services, economic value, role during several cropping cycles, etc) will be adopted and applied to each candidate species. The multifunctional value of each of these species can then be calculated on the basis of these selection criteria.
We are seeking a highly motivated, resourceful, and, above all, autonomous candidate. Strong skills and experience in bioinformatics, particularly in database management and development, are essential (Database Powered: PHP / MySQL / ORACLE / ASIAL, Programming languages and development tools: Python, GNU/Linux, Shell.). Knowledge of artificial intelligence–based tools, methods and NoSQL technologies would be considered an asset. Expertise in interaction biology, entomology, and plant biology will also be viewed favourably during the recruitment process.
Within the framework of this project, the recruited engineer will benefit from the ecological expertise of the ISA team. The current database is hosted by the Data Center of INRAE Toulouse (IT support: DSI-DATA-CENTER-INRAE), and collaboration with Nicolas Francillonne – URGI will provide access to a dedicated bioinformatics environment and expertise for digital tools management and development.
Applications, including a CV and a cover letter, should be sent as soon as possible to anne-violette.lavoir@inrae.fr and nicolas.francillonne@inrae.fr
1 Djian-Caporalino C. & Lavoir AV. 2024. Les plantes de services, Vers de nouveaux agroécosystèmes. Ed. QUAE.
Moreau, D., Ballini, E., Chave, M., Cordeau, S., Djian-Caporalino, C., Lavoir, A. V., Suffert, F. & Cortesero, A. M. (2025). Potential of service plants for regulating multiple pests while limiting disservices in agroecosystems. A review. Agronomy for Sustainable Development, 45(4), 1-32.
2 Boll R. & Lavoir A-V. 2023. BP-DB Biocontrol Plant Database, https://isaceaweb.sophia.inra.fr/bp_dss_dev/. Déclaration d’invention d’outils numériques n° IDDN.FR.001.510030.000.S.C.2023.000.10300
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